Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate WP_084936573.1 HA51_RS21365 sugar porter family MFS transporter
Query= SwissProt::P0AEP1 (464 letters) >NCBI__GCF_002095475.1:WP_084936573.1 Length = 464 Score = 764 bits (1972), Expect = 0.0 Identities = 386/462 (83%), Positives = 421/462 (91%), Gaps = 1/462 (0%) Query: 1 MPDAKKQGR-SNKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVS 59 MP + R SNK MT FVCFLAALAGLLFGLDIGVIAGALPFIA +F +T+H QEW+VS Sbjct: 1 MPGTTHKSRTSNKMMTLFVCFLAALAGLLFGLDIGVIAGALPFIAKDFNVTAHQQEWIVS 60 Query: 60 SMMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAV 119 SMMFGAAVGAVGSGW+S +LGRKKSLM GAILFV GSL+SA A + ++LI +RV+LGLAV Sbjct: 61 SMMFGAAVGAVGSGWMSSRLGRKKSLMAGAILFVIGSLWSAMATSPDMLIAARVVLGLAV 120 Query: 120 GVASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWRWMLGVIII 179 GVASYTAPLYLSEIAPEKIRGSMIS+YQLMITIGIL AYLSDTAFS GAWRWMLGVI I Sbjct: 121 GVASYTAPLYLSEIAPEKIRGSMISLYQLMITIGILAAYLSDTAFSDAGAWRWMLGVITI 180 Query: 180 PAILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGW 239 PAILLLIGVFFLP+SPRW AAK F A+RVL RLRDTS +AKRELDEIRESL++KQSGW Sbjct: 181 PAILLLIGVFFLPNSPRWLAAKGDFRSAQRVLDRLRDTSEQAKRELDEIRESLKIKQSGW 240 Query: 240 ALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLT 299 LF+ NS+FRRAV+LGVLLQVMQQFTGMNVIMYYAPKIFE+AG+ NTT+QMWGTVIVGL Sbjct: 241 QLFQSNSHFRRAVYLGVLLQVMQQFTGMNVIMYYAPKIFEIAGFANTTQQMWGTVIVGLV 300 Query: 300 NVLATFIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFI 359 NVLATFIAIGLVDRWGRKPTL LGF+VMAAGMG+LGTM+HIGIHS SAQYFA+AMLLMFI Sbjct: 301 NVLATFIAIGLVDRWGRKPTLVLGFIVMAAGMGILGTMLHIGIHSASAQYFAVAMLLMFI 360 Query: 360 VGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFW 419 VGFAMSAGPLIWVLCSEIQPLKGRDFGIT STATNWIANMIVGATFLTMLN+LGNA TFW Sbjct: 361 VGFAMSAGPLIWVLCSEIQPLKGRDFGITVSTATNWIANMIVGATFLTMLNSLGNAPTFW 420 Query: 420 VYAALNVLFILLTLWLVPETKHVSLEHIERNLMKGRKLREIG 461 VYA LNV FILLT+ L+PETK+VSLEHIERNLM G+KLR+IG Sbjct: 421 VYAGLNVFFILLTVALIPETKNVSLEHIERNLMSGKKLRDIG 462 Lambda K H 0.327 0.140 0.425 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 914 Number of extensions: 32 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 464 Length of database: 464 Length adjustment: 33 Effective length of query: 431 Effective length of database: 431 Effective search space: 185761 Effective search space used: 185761 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory